Rapid Elaboration of Fragments into Leads by X-ray Crystallographic Screening of Parallel Chemical Libraries (REFiL_X)

Abstract

A bottleneck in fragment-based lead development is the lack of systematic approaches to elaborate the initial fragment hits, which usually bind with low affinity to their target. Herein, we describe an analysis using X-ray crystallography of a diverse library of compounds prepared using microscale parallel synthesis. This approach yielded an 8-fold increase in affinity and detailed structural information for the resulting complex, providing an efficient and broadly applicable approach to early fragment development.

Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking

“…However, the best affinity of 279 mM reached is two orders of magnitude lower than in the campaign presented here. Also, compared with alternative approaches for the rapid elaboration of fragment hits, for example by screening diverse fragment follow-up compounds in crude reaction mixtures from fast chemistry (Baker et al, 2020;Bentley et al, 2020), the presented example campaign via Frag4Lead ended up with a similar number of hits and better affinity improvement. It seems rather obvious that these approaches could complement each other.…”

Structural bioinformatic analysis of DsbA proteins and their pathogenicity associated substrates

“…Secondly, DsbA is present in the periplasm, which is more accessible relative to cytoplasmic targets. Furthermore, all DsbA inhibitors described so far target the hydrophobic groove of DsbA [47] , [66] , [125] , [127] , [128] , [129] , [130] , which is not present in human thioredoxin or PDI. Therefore, despite DsbA belonging to the widespread thioredoxin superfamily, DsbA-tailored inhibitors are less likely to inhibit TRX-like proteins in humans.…”

“…Therefore, despite DsbA belonging to the widespread thioredoxin superfamily, DsbA-tailored inhibitors are less likely to inhibit TRX-like proteins in humans. The detailed analysis of the DsbA-substrate and DsbA-DsbB interactions described in this work could therefore inform a number of international campaigns in their efforts to designing specific inhibitors against DsbA enzymes [47] , [66] , [125] , [127] , [128] , [129] , [130] .…”

Racemases and epimerases operating through a 1,1-proton transfer mechanism: reactivity, mechanism and inhibition

“…227 Direct assaying of racemase or epimerase activity may also be possible using fluorescence anisotropy to monitor ligand binding. 227 Fragment screening using assays of enzyme activity 227,275-279 or biophysical techniques [275][276][277][278][279][280] (particularly X-ray crystallography [274][275][276][277][279][280][281] ) hold significant promise, although the different screening techniques have advantages and disadvantages 280 and different tendencies towards false positive and negative results. 279 There is also a balance to be struck between fragment complexity and affinity to maximise chances of success.…”